adding viloca to the workflow

[LaraFuhrmann]

No description provided.

[github-actions]

🦙 MegaLinter status: ✅ SUCCESS

Descriptor	Linter	Files	Fixed	Errors	Elapsed time
✅ BASH	shellcheck	11		0	0.59s
✅ DOCKERFILE	hadolint	1		0	0.32s
✅ JUPYTER	jupyfmt	3	0	0	2.64s
✅ MARKDOWN	markdownlint	11	0	0	0.98s
✅ PERL	perlcritic	1		0	1.04s
✅ PYTHON	black	62	1	0	1.96s
✅ SNAKEMAKE	snakefmt	25	1	0	8.8s

See detailed report in MegaLinter reports

MegaLinter is graciously provided by

[LaraFuhrmann]

Tested VILOCA on the hiv-tutorial data CAP188 4 using the following config files to test uniform-tiling strategy and amplicon tiling strategy.

general:
    virus_base_config: ""
    aligner: bwa
    snv_caller: viloca

input:
    reference: "{VPIPE_BASEDIR}/../resources/hiv/HXB2.fasta"
    metainfo_file: "{VPIPE_BASEDIR}/../resources/hiv/metainfo.yaml"
    gff_directory: "{VPIPE_BASEDIR}/../resources/hiv/gffs/"
    # NOTE: this input datadir isn't standard
    datadir: resources/samples/
    read_length: 301
    samples_file: samples.tsv
    paired: true

viloca:
    consensus: false

output:
    snv: true
    local: false
    global: false
    visualization: false
    QA: false

general:
    virus_base_config: ""
    aligner: bwa
    snv_caller: viloca

input:
    reference: "{VPIPE_BASEDIR}/../resources/hiv/HXB2.fasta"
    metainfo_file: "{VPIPE_BASEDIR}/../resources/hiv/metainfo.yaml"
    gff_directory: "{VPIPE_BASEDIR}/../resources/hiv/gffs/"
    # NOTE: this input datadir isn't standard
    datadir: resources/samples/
    read_length: 301
    samples_file: samples.tsv
    paired: true

viloca:
    consensus: false
    insert_bedfile: resources/samples/insert.bed

output:
    snv: true
    local: false
    global: false
    visualization: false
    QA: false